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- PDB-1dl3: CRYSTAL STRUCTURE OF MUTUALLY GENERATED MONOMERS OF DIMERIC PHOSP... -

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Basic information

Entry
Database: PDB / ID: 1dl3
TitleCRYSTAL STRUCTURE OF MUTUALLY GENERATED MONOMERS OF DIMERIC PHOSPHORIBOSYLANTRANILATE ISOMERASE FROM THERMOTOGA MARITIMA
ComponentsPROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
KeywordsISOMERASE / OLIGOMERISATION / THERMOSTABILITY / THERMOTOGA MARITIMA / PROTEIN ENGINEERING / DIMER EVOLUTION
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process
Similarity search - Function
N-(5'-phosphoribosyl)anthranilate isomerase family / N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsThoma, R. / Hennig, M. / Sterner, R. / Kirschner, K.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure and function of mutationally generated monomers of dimeric phosphoribosylanthranilate isomerase from Thermotoga maritima.
Authors: Thoma, R. / Hennig, M. / Sterner, R. / Kirschner, K.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
B: PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1394
Polymers45,9472
Non-polymers1922
Water57632
1
A: PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0692
Polymers22,9731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0692
Polymers22,9731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.680, 94.650, 46.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (PHOSPHORIBOSYLANTRANILATE ISOMERASE)


Mass: 22973.348 Da / Num. of mol.: 2 / Mutation: A25Y,F55E,I101W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET11C-TTRPF / Production host: Escherichia coli (E. coli) / Keywords: ENGINEERED MUTATION
References: UniProt: Q56320, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 1 MM EDTA 0.5 MM DTT 0.1 M HEPES/NAOH 16.7 MG/ML PROTEIN 0.75 M POTASSIUM DIHYDROGEN PHOSPHATE 0.75 M SODIUM DIHYDROGEN PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116.7 mg/mlprotein1drop
220 mMpotassium phosphate1drop
31 mMEDTA1drop
40.5 mMdithiothreitol1drop
50.75 Mpotassium dihydrogen phosphate1reservoir
60.75 Msodium dihydrogen phosphate1reservoir
70.1 MHEPES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 51809 / Num. obs: 11375 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.2
Reflection
*PLUS
Num. measured all: 51809
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.317

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.282 500 -RANDOM
Rwork0.175 ---
all-51809 --
obs-11375 99.2 %-
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 10 32 3128
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.5

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